CexoR-package: An R package to uncover high-resolution protein-DNA...

In CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Description

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.

Details

Package:	CexoR
Type:	Package
Version:	1.19.3
Date:	2018-07-03
License:	Artistic-2.0 | GPL-2 + file LICENSE
LazyLoad:	yes

Author(s)

Pedro Madrigal,

Maintainer: Pedro Madrigal [e-mail]

References

Madrigal P (2015) CexoR: an R/Bioconductor package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates. EMBnet.journal 21: e837.
Skellam JG (1946) The frequency distribution of the difference between two Poisson variates belonging to different populations. J R Stat Soc Ser A 109: 296.
Li Q, Brown J, Huang H, Bickel P (2011) Measuring reproducibility of high-throughput experiments. Ann Appl Stat 5: 1752-1779.
Rhee HS, Pugh BF (2011) Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147: 1408-1419.

Examples

## hg19. chr2:1-1,000,000. CTCF data from Rhee and Pugh (2011)

owd <- setwd(tempdir())

rep1 <- "CTCF_rep1_chr2_1-1e6.bam"
rep2 <- "CTCF_rep2_chr2_1-1e6.bam"
rep3 <- "CTCF_rep3_chr2_1-1e6.bam"
r1 <- system.file("extdata", rep1, package="CexoR",mustWork = TRUE)
r2 <- system.file("extdata", rep2, package="CexoR",mustWork = TRUE)
r3 <- system.file("extdata", rep3, package="CexoR",mustWork = TRUE)

chipexo <- cexor(bam=c(r1,r2,r3), chrN="chr2", chrL=1e6, idr=0.01, p=1e-12, N=3e4)

plotcexor(bam=c(r1,r2,r3), peaks=chipexo, EXT=500)

setwd(owd)

CexoR documentation built on Nov. 8, 2020, 11:04 p.m.